1mjp

X-ray diffraction
3.4Å resolution

METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR

Released:
Source organism: Escherichia coli
Primary publication:
Direct and indirect readout in mutant Met repressor-operator complexes.
Structure 8 905-14 (2000)
PMID: 10986458

Function and Biology Details

Reactions catalysed:
L-cystathionine + H(2)O = L-homocysteine + NH(3) + pyruvate
RX + glutathione = HX + R-S-glutathione
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
(1a) L-cystathionine = L-cysteine + 2-aminobut-2-enoate
ATP + kanamycin = ADP + kanamycin 3'-phosphate
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
ATP + a protein = ADP + a phosphoprotein
Maleate = fumarate
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
UDP-N-acetyl-alpha-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-hex-4-ulose + H(2)O
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
NTP + H(2)O = NDP + phosphate
D-ribose 5-phosphate = D-ribulose 5-phosphate
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
ATP-dependent cleavage of peptide bonds with broad specificity.
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
ATP + H(2)O = ADP + phosphate
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Met repressor Chains: A, B
Molecule details ›
Chains: A, B
Length: 104 amino acids
Theoretical weight: 12.03 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8U6 (Residues: 2-105; Coverage: 99%)
Gene names: JW3909, b3938, metJ
Sequence domains: Met Apo-repressor, MetJ
Structure domains: MET Apo-Repressor, subunit A
CONSENSUS OPERATOR DUPLEX Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Escherichia coli
Expression system: Not provided
CONSENSUS OPERATOR DUPLEX Chain: D
Molecule details ›
Chain: D
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P6222
Unit cell:
a: 118.39Å b: 118.39Å c: 83.71Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.226 0.309
Expression systems:
  • Escherichia coli
  • Not provided